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artic-network / artic-ncov2019

ARTIC nanopore protocol for nCoV2019 novel coronavirus
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artic assembly - Command failed:muscle -in & -out #93

Open AnyaKovalenko opened 2 years ago

AnyaKovalenko commented 2 years ago

Hello Everyone. Please could you help with the strange issue. After running the artic assembly (nanopolish) command in the end I see the following:

Running: muscle -in NB09_9.muscle.in.fasta -out NB09_9.muscle.out.fasta

Invalid command line
Unknown option in

Command failed:muscle -in NB09_9.muscle.in.fasta -out NB09_9.muscle.out.fasta

Can not find any answer regarding this muscle issue and what it means. I removed and installed the artic pipeline again but the same still exist. Please could somebody help. Many thanks.

iferres commented 2 years ago

Hi, I had the same issue. The problem is that muscle has been updated in conda to version 5.+ which is not backward compatible as it accept different arguments. The solution is to add the old version of muscle to the artic's environment.yml file and to rebuild the conda environment:

name: artic-ncov2019
channels:
  - conda-forge
  - bioconda
  - defaults
dependencies:
  - artic=1.2.1
  - artic-network::rampart=1.2.0
  - snakemake-minimal=5.8.1
  - muscle=3.8.1551
AnyaKovalenko commented 2 years ago

Thank @iferres so much. It is very helpful.